How to save settings before a factory reset?
By clicking the + next to the theme name you can save your current settings for your own theme. You can then select your theme after you choose factory default settings.



A gotcha with this is that the theme gets saved inside the blender installed files, so can be overwritten or deleted as blender is updated. To keep your theme for future versions you should find the saved file and move it into your configuration folder. Within the files installed for blender you will find your theme inside 2.75/scripts/presets/interface_theme (adjust 2.75 to match your current blender version). Locate your blender configuration folder and create a matching path and move your theme there. On a *nix system that would be $HOME/.config/blender/2.75/scripts/presets/interface_theme/MyTheme.xml